A tentative schedule of things we will do over the first few weeks. Link to the old Daily Schedule Summ14 Researcher's Names: see Summer 15 page Summer15 Lab Safety: Have you completed your lab safety trainings? Schedules: please enter your summer schedule here (e.g. classes that you may be taking in the summer or other conflicts with lab work) Mentors: Want to know when the mentors will be on? - check here Google Calendar Mentor Tasks: - see Mentors Summ 15 page using menu on the left
Research Presentations Schedule - see Journal Club Schedule
Summer Plasmids - for students to Transform and make more of this summer Lab Safety -- make sure you have done all the required lab safety training, print out your training record and put in the 3 ring binder Hours -
note the times that you are in lab on the paper sign in sheet at the front of lab. For Lab Safety concerns, we must have a running record of who is in the lab at which times. We will also use this to tally the total hours in lab for the summer.
THIS WEEK
General Items:
MENTORS:
Tally hours from last week and enter into spreadsheet on VDSStaff
RESEARCHERS:
Print Journal Club article for you and your friends
Update Lab Notebook & Wikispace page (for Tuesday night check)
- update your Google Page in the Google Drive folder /VDSclass/ResearchPages - this will automatically update the Wiki
REQUIRED ITEMS FOR NOTEBOOKS:
All practice cloning work (including well labelled gels)
Protein work (esp protein gel and FPLC output and nanodrop)
We definitely need all of your Target work to be present in the notebook.
DNA Works Output file - print the text file and past in notebook
Tail Primer Design (protocol and what you designed)
RE digest gel images, PCR gel images, Protein SDS-Page gels images
Nanodrop yields for your protein after purification (and after FPLC)
etc.
(TBD) Info from your Target Page (which means you need a Target page first!)
MaterialsSpreadsheets - is a new folder made in GDrive for:
Plasmid Concentrations
Protein Spectrophotometer Calcs
Solutions&DilutionsforGdocs
Week 8
Monday, July 27, 2015
12:30 - JC pre-meet
2:00 - Virtual Volunteers NDM-1 virtual drug screening
Tuesday, July 28, 2015
Wikispaces check.- due Tuesday night
Notebook check
- Charina will check them after 6pm (put line with date and comments in each)
Wednesday, July 29, 2015
2:00 - Virtual Volunteers NDM-1 virtual drug screening
Thursday, July 30, 2015
Lab Group Meeting @ 3:15 pm
GEA 100
Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups) Journal Club Summ 15
lab cleanup - clean up your samples (plates, PCR and RE digest tubes in -20degc, protein gel samples and purification samples)
Friday, July 31, 2015
last day of research
lab cleanup
NEXT WEEK
Dr. B NOTES:
Kevin H to do Pfu Polymerase and competent cells for extra
Coming Up Soonest:
students create folders in Mendeley for their targets - upload all relevant papers
all make PFU polymerase
Enzyme Inhibition Assay with YopH - all do it and then post graph of results.
Start competent cells protocol in teams of 2
New Members: Lab Safety Training, Pipetting Exercise, PyMol labs, Beer's Law lab, Virtual Screening 1 lab
VDS PCR
ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls
RE Digest
PCR pLIC
Protein Expression Trials with large scale (use Andee's, Charina's, Nikki's, Pfu Polymerase - Rachel & Parker)
Make Competent Cells
Lab Group Meeting @ 1 pm
GEA 100
Lab Notebook Check
Update Wikispaces - or change this to a Google Drive folder /VDSclass/ResearchProgress
each person make a page in GDocs called: ResearchProgress
Then 'COPY' this to the main Research Progress folder
UTEID_FirstNameLastInitial_ResearchProgress"
e.g. WEB31_WilliamB_ResearchProgress
Special Projects
Matthew S.
DNA sequencing for Fast targets
Transform NDM-1 plasmid to BL21(DE3) cells
Practice purification, characterization on old protein in -20 degC (I think it is Nikki's old one)
- work with Anita on this
On Fast Targets:
Create target pages for these on Wikispaces
Express, Purify, Characterize, FPLC, store,
enzyme assay test, DSF test
High Priority
NDM-1
Second Priority
IMP-7: (metal-dependent), pET-28b, His Tag
KPC-2: (serine beta lactamase), pET-24a, His Tag
VIM-2: (metal-dependent), pET-24a - No His Tag - Rachel and Parker to re-clone this into pNIC-Bsa4
Create target pages for these on Wikispaces
Express, Purify, Characterize, FPLC, store,
enzyme assay test, DSF test
Overall Flow:
Target Discovery
Design and Order primers for target
Practice Cloning Techniques
Practice large scale protein expression (Andee's target, YopH, RpFabG)
Make competent cells
Make Pfu polymerase for our cloning work
3-D printer items:
gel comb (1.0 mm for Bio-Rad)
FtHap and YopH models
Special Projects:
Fast NDM-1 screening (750), make protein first - maybe Anita
Fast target cloning - VIM-2
DSF on Fast Targets (and or YopH) - can we replicate Oscar's results (he has a protocol).
- IMP-7, VIM-2 (needs tag), KPC-2
Anita - DSF on YopH (need someone to make more protein with her guidance)
RpFabG
Research Tasks for Students:
make competent cells using Joey's protocol -
make PFU polymerase -
Dry Ice purchasing demo
Liguid Nitrogen purchasing demo
TACC tour
ITEMS IN GENERAL TO BE MAKING PROGRESS ON:
Enzyme assay on YopH or FtHap (whichever one you made)
Grow up pNIC-Bsa4 and MidiPrep (if you have not already done so)
Start cutting pNIC-Bsa4 with BsaI (store in freezer)
Lab clean up
- surfaces, fridges, old plates, old reagents, glassware
re-hang PDB Drug Poster
Organize powdered chemicals
Clean Stir bars
Fill & label spray bottles
Write items needed on whiteboard
Prep collirollers
Proper freezer box label orientation
SHOPPING! --- JOHN G has already done this
go to Fisher Chemistry Storeroom in WELCH. to get dry ice (bring a styrofoam container)
visit storerooms (walking by ICMB storeroom, then to biotech lab),
purchase the following items (see purchasing spreadsheet in GDocs /Misc/Purchasing) - PRINT IT OUT for 3 teams
- sharpies, spray bottles
- Taq DNA polymerase, 100bp and 1kb ladders
- Mini prep kit, midi prep kit, PCR cleanup kit, IPTG, DTT, TCEP
Enter purchase information in spreadsheet
Place receipt in Dr. B's 'receipt' cubby
prep new kits (midi, mini, PCR cleanup kits)
RESEARCHERS
Update Wikipages
Update notebooks:
Update Target page on Wikispaces (need all the info from the list of items) - if you don't have a Target page - start making it for your Target .
Fill out Travel Authorization Forms for field trips.
-- see GoogleDocs/Misc/TravelForms
-- print out and complete - put in Dr. B's box in lab (pigeon hole)
Then:
ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls
Print Journal Club article for you and your friends
Make LB for next week (500ml per person)
Agarose gel checks
Middle Schoolers visit lab
Mentors: prepare RE digest products for MSers
Cool Stuff We May Not Get To:
Library generation and ligand prep for virtual
Homology modelling
Screening with ICM
Lab Notebook check - should have everything up to date.
-- sleep all day
-- watch TV all day
Week 0
Friday, June 5, 2015 First meeting 1:00 PM - PAI 2.14 (the wet lab)
-- then we will walk over to GEA 100
After group meeting Tour of Places - led by John G & Andee (BioSci, ICMB, Comp labs, Biotech lab)
Get lab notebooks (see home page of Wikispaces for which type to get at the Coop)
Update your schedule on the GDrive spreadsheet
Create your own folder in Google Docs under the folder: /StudentFolders
Complete online Lab Safety training
Saturday, June 6, 2015- watch TV Sunday, June 7, 2015- watch TV
sign up for FF205 (firefighter training) Lab Safety classes
New guys - have lots of online classes to take too - see the link above
Print out safety training, hole punch and place in VDS sign in folder under the 'Safety' tab
Get lab notebooks (see home page of Wikispaces for which type to get at the Coop)
Update your schedule on the GDrive spreadsheet
Create your own folder in Google Docs under the folder: /StudentFolders
Complete online Lab Safety training
2 tasks:
1. Make LB
2. Dilute primers
1/2 of the group does LB with Andee while other half does Dilute primers with Nikki (or Charina) Then researchers switch and do the other thing
LB = either make 250 ml or 500 ml amounts depending on the available glassware (size of bottles)
Do this in pairs - write both names and other relevant information on the labels.
Andee to demonstrate autoclave usage ('See One')
Make LB and LB plates ProtocolLBAgarPlatesVDS.doc (VDS veterans)
LB plates (20ml per plates) -->
Andee picks:
3 people for Green
3 people for Red
3 people for Purple
3 people for pNIC-Bsa4
3 people for YopH pNIC-Bsa4
3 people for FtHap pNIC-Bsa4
Green, Red, Purple people make:
- 3 AMP plates (pair up or triple up - so that you are making 6 or 9 plates in a batch)
the rest make:
each person also needs 3 KAN plates (pair up or triple up so that you are making 4-6 plates in a batch)
while autoclave go to submit to DNA sequencing.
'Learn how to submit to DNA sequencing' (starring Andee et al.) - wet lab
ProtocolDNASequencingFacilityVDS_Summ15.doc
Sign up for a DNA sequenging [[#|account]] on DNA Lims.
submit pGBR22, pGFP, or pmCherry using forward or reverse primer - but not both
post results into the RESULTS folder of GDocs
After all of your safety training is posted to TxClass training History, Print out safety training, hole punch and place in VDS sign in folder under the 'Safety' tab
New people (don't worry about FF205 showing up on TxClass yet - go ahead and print out your training history verification for all the other safety classes)
New guys
- pipetting exercise and Buffers & Solutions (Lab 1 of Spring VDS)
Wednesday, June 10, 2015
Mathew S - sequence Fast targets
Target Discovery in computer lab - WEL 2.128
After all of your safety training is posted to TxClass training History, Print out safety training, hole punch and place in VDS sign in folder under the 'Safety' tab
New people (don't worry about FF205 showing up on TxClass yet - go ahead and print out your training history verification for all the other safety classes)
Thursday, June 11, 2015
Determine concentration of a plasmid (even if it already has it written on the tube!)
(- you pick: pGBR22 or pGFP or pmCherry or a pNIC-Bsa4 vector)
Nanodrop plasmid DNA - ProtocolNanoDropVDS.doc
Read the Journal Club article
Work on lab notebooks
Lab Notebook check - leave your notebook in lab (as always) when you are done around 5:00 pm
Charina will check these over.
Things to include:
What you have done each day
See the LabNotebook Grading rubric for rough guidelines. We don't need hypothesis for everything nor an extensive analysis - but you need the purpose or objective, the protocol, any results, and brief analysis or comments.
- Primer Dilution
- Lab safety training (if applicable)
- Making LB
- Making plates
- Submit to DNA sequencing
- Target Disco - generally address what we did - do not need to print and paste info though
GEA 100
1st Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups)
Zolli-Juran, M.; Cechetto, J. D.; Hartlen, R.; Daigle, D. M.; Brown, E. D., High throughput screening identifies novel inhibitors of Escherichia coli dihydrofolate reductase that are competitive with dihydrofolate. Bioorganic & Medicinal Chemistry Letters 2003, 13 (15), 2493-2496. Zolli_JuranDHFRbacteriaHTSBioorgMedChemLett2003.pdf
Fill out Travel Authorization Forms for field trips.
-- see GoogleDocs/Misc/TravelForms
-- print out and complete - put in Dr. B's box in lab (pigeon hole)
Matthew S. - transform NDM-1, + 2 other lactamase targets
Target Disco con't.....
Analyze DNA Sequence Exercise as a group ?
in the Google Drive folder /VDSclass/ResearchProgress
each person make a page in GDocs called: ResearchProgress
Then 'COPY' this to the main Research Progress folder so that it can be seen in both places - your folder and in the shared ResearchProgress folder
Saturday, June 13, 2015 - watch TV Sunday, June 14, 2015 - watch TV
Post data/results to your Wikispaces page - Summer15
Week 2
Monday, June 15, 2015
Target Disco con't.....
Analyze DNA Sequence Exercise as a group ?
Oligo Primer Design
Fill out Travel Authorization Forms for field trips.
-- see GoogleDocs/Misc/TravelForms
There are two forms:
1. Release
2. Medical Authorization
-- if you are a Minor - do the ones for minors.
-- if you are an adult - do the ones for adults
-- print out and complete - put in Dr. B's box in lab (pigeon hole)
Photo Release Forms too (or did we already do these?)
Matthew S - start protein expression of NDM-1 with Anita in the AM
- Parker/Rachel to spin down on Tuesday evening
Ashley - Transform Pfu Polymerase (Amp or Kan - I don't know - view protocol on our ProteinProtocols to figure out.)
- NOTE: this actually needs to be done into BL21(DE3) cells !!!! because it will be for protein expression.
Need 1.6 L of LB - check to see if we have enough
start o/n culture of colonies for Midi-preps
- 2 x 80ml of LB for High Copy plasmids (happens to be the Amp ones for us) -
(80ml is one 'culture's worth. The other 80 ml is a backup)
- 1 x 160 ml of LB for Low Copy plasmids (happens to be the Kan ones for us)-
(160ml is one culture's worth. The other 160ml would be a backup, but we don't have enough room in the incubator)
Do this in Pairs (Andee to assign)
2 pGBR22
1 GFP
1 pmCherry
4 - pNIC-Bsa4
1 - EhPTP
1 - Pv6PG
Anthony + Lisa
pNIC-Bsa4
Diane + Matthew N
EhPTP
Ashley + Bella
pGBR22
Kevin H + Mayur
pGBR22
Justin + Bethany
pNIC-Bsa4
Simone + Ana
Pv6PG
Kevin N +
Parker/Rachael
pmcherry
Krupa + Arthi
pNIC-Bsa4
Steven + (Priya)
pNIC-Bsa4
Jeff + Hannah
pGFP
NOTE: the Kan or Amp is not what makes them high or low copy. It is a function of the plasmid. You get more copies of DNA made from a high copy plasmid.
Follow this protocol for the following plasmids: pGBR22, pGFP, pmCherry
ProtocolTransformationforPlasmidPrepVDS.doc
Follow this protocol for the following plasmids: pNic-Bsa4
ProtocolTransformationforPlasmidPrep_pNIC_Bsa4_VDS_v4
Tuesday, June 16, 2015
count colonies & calculate Transformation Efficiency from last week - put in Lab Notebook with Pics.
Upload pics to your Google Research Page/ Wiki.
check DNA sequencing results - put on Wiki and in notebook
-- Mentor to do lab safety training sheet tally - see if each researcher has their sheet pasted in the binder, then enter their name on the Wiki page
Make 20% sucrose - and sterile filter it - DONE
Make Kan/Sucrose (5%) plates - 2 per person
Andee - buy Midi-Prep kit?
GROUP 2
- comes in to make plates
-make Buffers for competent cells protocol
- then proceeed to MidiPrep
If time,
Make IPTG - sterile filter, aliquot into 1.6 ml centrifuge tubes with 500 ul in each. ---- 1 M IPTG in nanopure
Andee
Spin downs (do in waves, not all at once)
Midi-preps (group 1)
Group 1
Anthony + Lisa
pNIC-Bsa4
Diane + Matthew N
EhPTP
Steven + (Priya)
pNIC-Bsa4
Kevin H + Mayur
pGBR22
Justin + Bethany
pNIC-Bsa4
For Group 1 who have finished Midi-Prep - proceed to transformations.
Transformations into BL21(DE3) cells for Protein Expression:
w/ Kan plates
Andee's Target
Charina's Target
Nikki's Target
Charina's at 4:30 pm
Midi-preps (group 2)
Group 2
Simone + Ana
Pv6PG
Kevin N +
Parker/Rachael
pmcherry
Krupa + Arthi
pNIC-Bsa4
Ashley + Bella
pGBR22
Jeff + Hannah
pGFP
Charina's group won't do transformations
-
Wednesday, June 17, 2015
Midiprep - Group 1
After - Nanodrop, then submit sample to DNA sequencing
Transformation of plasmids for protein prep - Group 2
Charinas
Nikkis
Andee
Oscar's
Midiprep - Group 2
After - Nanodrop, then submit sample to DNA sequencing
HSers - Buffers & Solutions lab
2pm - Middle Schoolers visit lab (2 of them)
Nikki to work with them (pre-make a gel), do calculations of plasmid amounts beforehand
- brief intro, make gel, practice pipetting, pipette samples into tubes, pipette samples into gel and run, image gel and analyze
- samples: both DNA ladders, several plasmids of different sizes. I would run 300 ng of each.
Dry Ice Tour - with Tonita
Liquid Nitrogen Tour - with Tonita
Target Disco con't.....
Oligo Primer Design
Parker/Rachel - spin down Matthew's samples (at 18-20 hrs after induction with IPTG)
Parker/Rachel - Grow up colonies of PFU polymerase for test - DOES IT GROW OVERNIGHT?
- start 2x 5ml LB overnight culture of Pfu colonies in Amp (use existing plate)
(get mentor help - or from Anita/Tony a.k.a. 'Tonita')
Thursday, June 18, 2015
Pre-meeting for Journal Club presenters with Dr. B - 12:00 in his office.
Read journal article
Remove plates from incubator and move to fridge (for those that did transformation yesterday)
RE Digest
Analyze DNA Sequence Exercise as a group ?
Make and run gel for RE Digest (use Agarose Gel protocol)
????
My first PCR - Group 1
My first PCR - Group 2 (if time)
Target Discovery selections
Protocol Primer Design OverlapAssembly
Order Overlap Primers for class
On Your Targets Page:
Add Link to DNA Works output text file
Add substrate cost, quantity, and catalog numbers (and supplier) for enzyme assay reagents
Add image of BRENDA reaction mechanism (screenshot it)
Update your lab notebook for this Week - ALL
Update your weekly Wikispaces Research page - ALL
Saturday, June 20, 2015 Sunday, June 21, 2015
Thursday, June 25, 2015
VisLab Tour @ 2 pm POB 2.404
Lab Group Meeting @ 1 pm
GEA 100
1st Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups)
Zolli-Juran, M.; Cechetto, J. D.; Hartlen, R.; Daigle, D. M.; Brown, E. D., High throughput screening identifies novel inhibitors of Escherichia coli dihydrofolate reductase that are competitive with dihydrofolate. Bioorganic & Medicinal Chemistry Letters 2003, 13 (15), 2493-2496. Zolli_JuranDHFRbacteriaHTSBioorgMedChemLett2003.pdf
Post data/results to your Wikispaces page - Summer15
update your Google Page in the Google Drive folder /VDSclass/ResearchPages - this will automatically update the Wiki
REQUIRED ITEMS FOR NOTEBOOKS:
All practice cloning work (including well labelled gels)
Info from your Target Page (which means you need a Target page first!)
Monday, June 22, 2015
protein expressions in Groups
Tuesday, June 23, 2015
protein expressions in Groups, con't.....
Wednesday, June 24, 2015
- HOSA - Nikki, Charina
Middle Schoolers visit lab (2-4 pm)
Make Homemade SDS-Page gels (stagger) - how many plates do we have?
Target selection & Ordering Primers
Make buffers for purification - stagger
My First PCR - stagger (maybe)
Thursday, June 25, 2015
- HOSA - Nikki, Charina
Make Homemade SDS-Page gels (stagger) - how many plates do we have?
Make buffers for purification - stagger
Purifications
My First PCR - stagger
TACC VisLab Tour @ 2 pm POB 2.404
Friday, June 26, 2015
- HOSA - Nikki, Charina
Lab Group Meeting @ 1 pm
GEA 100
Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups) Journal Club Summ 15
Post data/results to your Wikispaces page - Summer15
update your Google Page in the Google Drive folder /VDSclass/ResearchPages - this will automatically update the Wiki
Purifications
Target Disco con't.....
Oligo Primer Design
Purifications
REQUIRED ITEMS FOR NOTEBOOKS:
All practice cloning work (including well labelled gels)
Protein work (esp protein gel and FPLC output and nanodrop)
We definitely need all of your Target work to be present in the notebook.
DNA Works Output file - print the text file and past in notebook
Tail Primer Design (protocol and what you designed)
Info from your Target Page (which means you need a Target page first!)
Saturday, June 27, 2015 Sunday, June 28, 2015
Week 4
Monday, June 29, 2015
Lab Hours totaling (Charina or Nikki)
Wikispaces check - Nikki (put commments on each one)
Notebook check - Charina
FPLC - Matthew S. (and other VDSers will watch to learn the process - and get a 'See One' checkoff)
Transform, grow up in 160ml of LB+Kan, Midi-prep:
Diane - IMP-7 in pET28b
Anthony - KPC2 in pet24a
Simone - VIM2 in pet24a
Make SDS-PAGE gels - everyone that needs to
Run SDS-PAGE gels
Tuesday, June 30, 2015
My First PCR
Spin samples to prep for FPLC on Wed or Thurs
- store in 4degC
Wednesday, July 1, 2015
Target picking ?
TACC Tour
We will all meet at 1:00 pm to walk to the BUS together as a group.
We will be back on campus around 4 or 5pm https://www.tacc.utexas.edu/about/contact Thursday, July 2, 2015
FPLC
Lab Group Meeting @ 1 pm
GEA 100
Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups) Journal Club Summ 15
Update your notebook for the week
Post data/results to your Wikispaces page
- update your Google Page in the Google Drive folder /VDSclass/ResearchPages - this will automatically update the Wiki
Friday, July 3, 2015
Optional day - no new stuff, time to catch up on things you haven't gotten done.
Saturday, July 4, 2015 - Happy 4th of July! Sunday, July 5, 2015
Week 5 OVERVIEW:
Protein expression work (FPLC),
starting 2nd protein expression
2nd Practice PCR
Design Tail Primers, Make Oligo Mix
Make Competent Cells (in pairs)
Monday, July 6, 2015
Lab Hours totaling (Nikki)
Target Selections - fill out form to select your target
Verify HIS tags on beta-metallo lactamases - Diane & Anthony & Simone
- use the Translation Map functinality of the Sequence Manipulation Suite to help http://www.bioinformatics.org/sms2/index.html
- need a WORD document with highlighted regions
If your protein 'worked' from last week, then concentrate protein samples for FPLC.
The protein groups should work together. E.g. the two RpFabG groups would both concentrate their samples separately, but then combine them for FPLC.
FPLC - see FPLC ToDo groups above
Second Practice PCR (after you have done My First PCR successfully)
- PCR pLICsequencing15.xls
2:00 PM - Virtual Volunteers (NDM-1) in computer lab
- gather control compounds
- start some screening
What are the Magical Mystery Genes inside of pNIC-Bsa4?
- send pNIC-Bsa4 to sequencing using pLIC for and pLIC rev.
Start overnight cultures of 2nd Protein Expression
- (alternatively, start them in the morning depending on which Option you choose to do (A or B))
Tuesday, July 7, 2015
Start protein expression Round 2 - if you chose morning Option.
Continue PCRs At end of day -
Wikispaces check.- due Tuesday night (Dr. B to check)
Notebook check
- Charina will check them after 6pm (put line with date and comments in each)
Wednesday, July 8, 2015
Stop Waste flow on FPLC Machine (Andee)
-check on pressure
Concentrate protein samples
FPLC - see FPLC ToDo groups abov
2-4 PM - Middle Schoolers visit lab - Lisa & Simone host
Thursday, July 9, 2015
12:00 - Fellowship photo shoot on front steps of PAI
Concentrate protein samples
FPLC - see FPLC ToDo groups above
4:00 pm - Tail Primer Design Session (in computer lab with Dr. B)
Friday, July 10, 2015
Lab Group Meeting @ 1 pm
GEA 100
Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups) Journal Club Summ 15
Update your notebook for the week
Post data/results to your Wikispaces page
- update your Google Page in the Google Drive folder /VDSclass/ResearchPages - this will automatically update the Wiki
2:15 - Lab Tour by Nikki for prospective students
3:30 PM - Virtual Volunteers (NDM-1) in computer lab
- gather control compounds
- set up proteins in GOLD
- start some screening
Oligo Primer dilution (each person makes their own Oligo Mix to use)
Saturday, July 11, 2015 Sunday, July 12, 2015
FPLC COMPLETED:
MtDdla
Ashley C.
Lisa S.
FPLC ToDo:
EhPTP
Anthony A. - Kevin H.
Ana R. - Justin H.
MtDdla
Kevin N.
Hannah K.
Pv6PG
Diane C. - Bella D.
Arthi K. - Simone M.
RpFabG
Bethany R. - Matthew N.
Parker D. - Jeffrey X.
Pfu Polymerase
Krupa S. - Mayur P. - Priya M.
Steven T. - Rachael B.
Week 6 OVERVIEW:
Protein expression work (FPLC),
finish 2nd protein expression
Make Oligo Mix
Make pNIC-Bsa4, midiprep it, send to sequencing, cut with BsaI for cloning
sequence using pLIC for and pLIC rev.
Make Pfu Polymerase
Make Competent Cells (in pairs)
Week 6
Monday, July 13, 2015
1:00 - Virtual Volunteers NDM-1 virtual drug screening - finish ligand prep for controls - prep proteins in GOLD - dock control ligands - compare results for control set - start runs of libraries
Oligo Primer dilution (each person makes their own Oligo Mix to use)
Primary PCR
Tuesday, July 14, 2015
Oligo Primer dilution (each person makes their own Oligo Mix to use)
Primary PCR
At end of day -
Wikispaces check.- due Tuesday night (Dr. B to check)
Notebook check
- Charina will check them after 6pm (put line with date and comments in each)
Wednesday, July 15, 2015
grow up ovenight culture of pNIC-Bsa4 (160ml of LB). Either save in freezer in the morning, or midi-prep it.
Thursday, July 16, 2015
3:20 - meet in lab and we'll walk over to PCL as a group
3:30- 4:30 PM - Roxanne Bogucka - Literature reading instruction activity (with the Aptamer stream! - PCL 1.124
Once you have your pNIC-Bsa4 sequencing back, What are the Magical Mystery Genes inside of pNIC-Bsa4?
- send pNIC-Bsa4 to sequencing using pLIC for and pLIC rev.
Friday, July 17, 2015
Lab Group Meeting @ 1 pm
GEA 100
Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups) Journal Club Summ 15
Work on Target Pages in Wkispaces (Target pages vs. Research Pages)
Saturday, July 18, 2015 Sunday, July 19, 2015
Week 7
OVERVIEW:
finish 2nd protein expression
Make pNIC-Bsa4, midiprep it, send to sequencing, cut with BsaI for cloning
sequence using pLIC for and pLIC rev.
Make Pfu Polymerase
Monday, July 20, 2015 1:00 - Virtual Volunteers NDM-1 virtual drug screening
Tuesday, July 21, 2015
Yes, yes - the cloning protocol is finally uploaded to GDrive/Protocols
At end of day -
Wikispaces check.- due Tuesday night (Dr. B to check)
Notebook check
- Charina will check them after 6pm (put line with date and comments in each)
Wednesday, July 22, 2015
1 PM - Virtual Screening - generate a final list of NDM-1 inhibitor candidates
Thursday, July 23, 2015
UT Honors Colloquium for visiting HS students to UT - Lisa and Charina to attend and represent FRI.
1:00 - Virtual Volunteers - finalize NDM-1 list of compounds to submit to Dr. Fast
Documentary viewing at 4:00 in PAI 3.00? lecture hall
Friday, July 24, 2015
Lab Group Meeting @ 1 pm
GEA 100
Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups) Journal Club Summ 15
Work on Target Pages in Wkispaces (Target pages vs. Research Pages) Saturday, July 25, 2015 Sunday, July 26, 2015
Researcher's Names: see Summer 15 page Summer15
Lab Safety: Have you completed your lab safety trainings?
Schedules: please enter your summer schedule here (e.g. classes that you may be taking in the summer or other conflicts with lab work)
Mentors: Want to know when the mentors will be on? - check here Google Calendar
Mentor Tasks: - see Mentors Summ 15 page using menu on the left
Journal Club Presentations Schedule
Research Presentations Schedule - see Journal Club Schedule
Summer Plasmids - for students to Transform and make more of this summerLab Safety -- make sure you have done all the required lab safety training, print out your training record and put in the 3 ring binder
Hours -
note the times that you are in lab on the paper sign in sheet at the front of lab. For Lab Safety concerns, we must have a running record of who is in the lab at which times. We will also use this to tally the total hours in lab for the summer.
THIS WEEK
General Items:MENTORS:
Tally hours from last week and enter into spreadsheet on VDSStaff
RESEARCHERS:
Print Journal Club article for you and your friends
Update Lab Notebook & Wikispace page (for Tuesday night check)
- update your Google Page in the Google Drive folder /VDSclass/ResearchPages - this will automatically update the Wiki
REQUIRED ITEMS FOR NOTEBOOKS:
All practice cloning work (including well labelled gels)
Protein work (esp protein gel and FPLC output and nanodrop)
We definitely need all of your Target work to be present in the notebook.
MaterialsSpreadsheets - is a new folder made in GDrive for:
Week 8
Monday, July 27, 201512:30 - JC pre-meet
2:00 - Virtual Volunteers NDM-1 virtual drug screening
Tuesday, July 28, 2015
Wikispaces check.- due Tuesday night
Notebook check
- Charina will check them after 6pm (put line with date and comments in each)
Wednesday, July 29, 2015
2:00 - Virtual Volunteers NDM-1 virtual drug screening
Thursday, July 30, 2015
Lab Group Meeting @ 3:15 pm
GEA 100Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups)
Journal Club Summ 15
lab cleanup - clean up your samples (plates, PCR and RE digest tubes in -20degc, protein gel samples and purification samples)
Friday, July 31, 2015
last day of research
lab cleanup
NEXT WEEK
Dr. B NOTES:
Kevin H to do Pfu Polymerase and competent cells for extra
Coming Up Soonest:
students create folders in Mendeley for their targets - upload all relevant papers
all make PFU polymerase
Enzyme Inhibition Assay with YopH - all do it and then post graph of results.
Start competent cells protocol in teams of 2
New Members: Lab Safety Training, Pipetting Exercise, PyMol labs, Beer's Law lab, Virtual Screening 1 lab
VDS PCR
ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls
RE Digest
PCR pLIC
Protein Expression Trials with large scale (use Andee's, Charina's, Nikki's, Pfu Polymerase - Rachel & Parker)
Make Competent Cells
Lab Group Meeting @ 1 pm
GEA 100Lab Notebook Check
Update Wikispaces - or change this to a Google Drive folder /VDSclass/ResearchProgress
each person make a page in GDocs called: ResearchProgress
Then 'COPY' this to the main Research Progress folder
UTEID_FirstNameLastInitial_ResearchProgress"
e.g. WEB31_WilliamB_ResearchProgress
Special Projects
Matthew S.
DNA sequencing for Fast targets
Transform NDM-1 plasmid to BL21(DE3) cells
Practice purification, characterization on old protein in -20 degC (I think it is Nikki's old one)
- work with Anita on this
On Fast Targets:
Create target pages for these on Wikispaces
Express, Purify, Characterize, FPLC, store,
enzyme assay test, DSF test
High Priority
NDM-1
Second Priority
IMP-7: (metal-dependent), pET-28b, His Tag
KPC-2: (serine beta lactamase), pET-24a, His Tag
VIM-2: (metal-dependent), pET-24a - No His Tag - Rachel and Parker to re-clone this into pNIC-Bsa4
Create target pages for these on Wikispaces
Express, Purify, Characterize, FPLC, store,
enzyme assay test, DSF test
Overall Flow:
Target Discovery
Design and Order primers for target
Practice Cloning Techniques
Practice large scale protein expression (Andee's target, YopH, RpFabG)
Make competent cells
Make Pfu polymerase for our cloning work
3-D printer items:
Special Projects:
Fast NDM-1 screening (750), make protein first - maybe Anita
Fast target cloning - VIM-2
DSF on Fast Targets (and or YopH) - can we replicate Oscar's results (he has a protocol).
- IMP-7, VIM-2 (needs tag), KPC-2
Anita - DSF on YopH (need someone to make more protein with her guidance)
RpFabG
Research Tasks for Students:
make competent cells using Joey's protocol -
make PFU polymerase -
Dry Ice purchasing demo
Liguid Nitrogen purchasing demo
TACC tour
ITEMS IN GENERAL TO BE MAKING PROGRESS ON:
Enzyme assay on YopH or FtHap (whichever one you made)
Grow up pNIC-Bsa4 and MidiPrep (if you have not already done so)
Start cutting pNIC-Bsa4 with BsaI (store in freezer)
Lab clean up
- surfaces, fridges, old plates, old reagents, glassware
re-hang PDB Drug Poster
Organize powdered chemicals
Clean Stir bars
Fill & label spray bottles
Write items needed on whiteboard
Prep collirollers
Proper freezer box label orientation
SHOPPING! --- JOHN G has already done this
go to Fisher Chemistry Storeroom in WELCH. to get dry ice (bring a styrofoam container)
visit storerooms (walking by ICMB storeroom, then to biotech lab),
purchase the following items (see purchasing spreadsheet in GDocs /Misc/Purchasing) - PRINT IT OUT for 3 teams
- sharpies, spray bottles
- Taq DNA polymerase, 100bp and 1kb ladders
- Mini prep kit, midi prep kit, PCR cleanup kit, IPTG, DTT, TCEP
Enter purchase information in spreadsheet
Place receipt in Dr. B's 'receipt' cubby
prep new kits (midi, mini, PCR cleanup kits)
RESEARCHERS
Update Wikipages
Update notebooks:
Update Target page on Wikispaces (need all the info from the list of items) - if you don't have a Target page - start making it for your Target .
Fill out Travel Authorization Forms for field trips.
-- see GoogleDocs/Misc/TravelForms
-- print out and complete - put in Dr. B's box in lab (pigeon hole)
Then:
ProtocolPCRforREcloningGREEN.xls OR ProtocolPCRforREcloningRED.xls
Print Journal Club article for you and your friends
Make LB for next week (500ml per person)
Agarose gel checks
Middle Schoolers visit lab
Cool Stuff We May Not Get To:
Library generation and ligand prep for virtual
Homology modelling
Screening with ICM
- pharmacophore models
DSF (Differential Scanning Fluorimetry) assaysqPCR
Crystallization trials
Staff Stuff:
Label new reagents and supplies
Dilute new 100 bp ladder in Blue Juice + TE
Target Discovery choices --> order primer sets
ToDo List:
Lab Notebook Checks
Protocol cost analysis (Transformation, cloning)
Walk through |protein expression (use current mentor's enzymes)
T-shirt Form for VDS shirts
??????
Lab Notebook check - should have everything up to date.
-- sleep all day
-- watch TV all day
Week 0
Friday, June 5, 2015First meeting 1:00 PM - PAI 2.14 (the wet lab)
-- then we will walk over to GEA 100
After group meeting
Tour of Places - led by John G & Andee (BioSci, ICMB, Comp labs, Biotech lab)
Get lab notebooks (see home page of Wikispaces for which type to get at the Coop)
Update your schedule on the GDrive spreadsheet
Create your own folder in Google Docs under the folder: /StudentFolders
Complete online Lab Safety training
Saturday, June 6, 2015 - watch TV
Sunday, June 7, 2015 - watch TV
Week 1
Monday, June 8, 2015Start time: 12:30
Lab Safety training - for those new to the lab (HS and ACC)
- walk through with the mentors (Andee, Charina and/or Nikki)
http://vdsstream.wikispaces.com/Required+Lab+Safety
Get lab notebooks (see home page of Wikispaces for which type to get at the Coop)
Update your schedule on the GDrive spreadsheet
Create your own folder in Google Docs under the folder: /StudentFolders
Complete online Lab Safety training
2 tasks:
1. Make LB
2. Dilute primers
1/2 of the group does LB with Andee while other half does Dilute primers with Nikki (or Charina)
Then researchers switch and do the other thing
LB = either make 250 ml or 500 ml amounts depending on the available glassware (size of bottles)
Do this in pairs - write both names and other relevant information on the labels.
Andee to demonstrate autoclave usage ('See One')
Dilute some primers - with Nikki or Charina
Tuesday, June 9, 2015
Low Key day - Andee to lead
Make LB and LB plates ProtocolLBAgarPlatesVDS.doc (VDS veterans)
LB plates (20ml per plates) -->
Andee picks:
3 people for Green
3 people for Red
3 people for Purple
3 people for pNIC-Bsa4
3 people for YopH pNIC-Bsa4
3 people for FtHap pNIC-Bsa4
Green, Red, Purple people make:
- 3 AMP plates (pair up or triple up - so that you are making 6 or 9 plates in a batch)
the rest make:
each person also needs 3 KAN plates (pair up or triple up so that you are making 4-6 plates in a batch)
while autoclave go to submit to DNA sequencing.
'Learn how to submit to DNA sequencing' (starring Andee et al.) - wet lab
After all of your safety training is posted to TxClass training History, Print out safety training, hole punch and place in VDS sign in folder under the 'Safety' tab
New guys
- pipetting exercise and Buffers & Solutions (Lab 1 of Spring VDS)
Wednesday, June 10, 2015
Mathew S - sequence Fast targets
Target Discovery in computer lab - WEL 2.128
After all of your safety training is posted to TxClass training History, Print out safety training, hole punch and place in VDS sign in folder under the 'Safety' tab
Thursday, June 11, 2015
Determine concentration of a plasmid (even if it already has it written on the tube!)
(- you pick: pGBR22 or pGFP or pmCherry or a pNIC-Bsa4 vector)
Read the Journal Club article
Work on lab notebooks
Lab Notebook check - leave your notebook in lab (as always) when you are done around 5:00 pm
Charina will check these over.
Things to include:
What you have done each day
See the LabNotebook Grading rubric for rough guidelines. We don't need hypothesis for everything nor an extensive analysis - but you need the purpose or objective, the protocol, any results, and brief analysis or comments.
- Primer Dilution
- Lab safety training (if applicable)
- Making LB
- Making plates
- Submit to DNA sequencing
- Target Disco - generally address what we did - do not need to print and paste info though
Transformations ?
Input information about which culture of plasmid you have (or will) grow up.
http://vdsstream.wikispaces.com/Summer+Plasmids
Friday, June 12, 2015
Lab Group Meeting @ 1 pm
GEA 1001st Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups)
Zolli-Juran, M.; Cechetto, J. D.; Hartlen, R.; Daigle, D. M.; Brown, E. D., High throughput screening identifies novel inhibitors of Escherichia coli dihydrofolate reductase that are competitive with dihydrofolate. Bioorganic & Medicinal Chemistry Letters 2003, 13 (15), 2493-2496.
Zolli_JuranDHFRbacteriaHTSBioorgMedChemLett2003.pdf
Fill out Travel Authorization Forms for field trips.
-- see GoogleDocs/Misc/TravelForms
-- print out and complete - put in Dr. B's box in lab (pigeon hole)
Matthew S. - transform NDM-1, + 2 other lactamase targets
Target Disco con't.....
Analyze DNA Sequence Exercise as a group ?
in the Google Drive folder /VDSclass/ResearchProgress
each person make a page in GDocs called: ResearchProgress
Then 'COPY' this to the main Research Progress folder so that it can be seen in both places - your folder and in the shared ResearchProgress folder
Saturday, June 13, 2015 - watch TV
Sunday, June 14, 2015 - watch TV
Post data/results to your Wikispaces page - Summer15
Week 2
Monday, June 15, 2015Target Disco con't.....
Analyze DNA Sequence Exercise as a group ?
Oligo Primer Design
Fill out Travel Authorization Forms for field trips.
-- see GoogleDocs/Misc/TravelForms
There are two forms:
1. Release
2. Medical Authorization
-- if you are a Minor - do the ones for minors.
-- if you are an adult - do the ones for adults
-- print out and complete - put in Dr. B's box in lab (pigeon hole)
Photo Release Forms too (or did we already do these?)
Matthew S - start protein expression of NDM-1 with Anita in the AM
- Parker/Rachel to spin down on Tuesday evening
Ashley - Transform Pfu Polymerase (Amp or Kan - I don't know - view protocol on our ProteinProtocols to figure out.)
- NOTE: this actually needs to be done into BL21(DE3) cells !!!! because it will be for protein expression.
Need 1.6 L of LB - check to see if we have enough
start o/n culture of colonies for Midi-preps
- 2 x 80ml of LB for High Copy plasmids (happens to be the Amp ones for us) -
(80ml is one 'culture's worth. The other 80 ml is a backup)
- 1 x 160 ml of LB for Low Copy plasmids (happens to be the Kan ones for us)-
(160ml is one culture's worth. The other 160ml would be a backup, but we don't have enough room in the incubator)
Do this in Pairs (Andee to assign)
2 pGBR22
1 GFP
1 pmCherry
4 - pNIC-Bsa4
1 - EhPTP
1 - Pv6PG
Parker/Rachael
NOTE: the Kan or Amp is not what makes them high or low copy. It is a function of the plasmid. You get more copies of DNA made from a high copy plasmid.
Follow this protocol for the following plasmids: pGBR22, pGFP, pmCherry
ProtocolTransformationforPlasmidPrepVDS.doc
Follow this protocol for the following plasmids: pNic-Bsa4
ProtocolTransformationforPlasmidPrep_pNIC_Bsa4_VDS_v4
Tuesday, June 16, 2015
count colonies & calculate Transformation Efficiency from last week - put in Lab Notebook with Pics.
Upload pics to your Google Research Page/ Wiki.
check DNA sequencing results - put on Wiki and in notebook
-- Mentor to do lab safety training sheet tally - see if each researcher has their sheet pasted in the binder, then enter their name on the Wiki page
Make 20% sucrose - and sterile filter it - DONE
Make Kan/Sucrose (5%) plates - 2 per person
Andee - buy Midi-Prep kit?
GROUP 2
- comes in to make plates
-make Buffers for competent cells protocol
- then proceeed to MidiPrep
If time,
Make IPTG - sterile filter, aliquot into 1.6 ml centrifuge tubes with 500 ul in each.
---- 1 M IPTG in nanopure
Andee
Spin downs (do in waves, not all at once)
Midi-preps (group 1)
For Group 1 who have finished Midi-Prep - proceed to transformations.
Transformations into BL21(DE3) cells for Protein Expression:
w/ Kan platesAndee's Target
Charina's Target
Nikki's Target
Charina's at 4:30 pm
Midi-preps (group 2)
Parker/Rachael
Charina's group won't do transformations
-
Wednesday, June 17, 2015
Midiprep - Group 1
After - Nanodrop, then submit sample to DNA sequencing
Transformation of plasmids for protein prep - Group 2
Charinas
Nikkis
Andee
Oscar's
Midiprep - Group 2
After - Nanodrop, then submit sample to DNA sequencing
HSers - Buffers & Solutions lab
2pm - Middle Schoolers visit lab (2 of them)
Nikki to work with them (pre-make a gel), do calculations of plasmid amounts beforehand
- brief intro, make gel, practice pipetting, pipette samples into tubes, pipette samples into gel and run, image gel and analyze
- samples: both DNA ladders, several plasmids of different sizes. I would run 300 ng of each.
Dry Ice Tour - with Tonita
Liquid Nitrogen Tour - with Tonita
Target Disco con't.....
Oligo Primer Design
Parker/Rachel - spin down Matthew's samples (at 18-20 hrs after induction with IPTG)
Parker/Rachel - Grow up colonies of PFU polymerase for test - DOES IT GROW OVERNIGHT?
- start 2x 5ml LB overnight culture of Pfu colonies in Amp (use existing plate)
(get mentor help - or from Anita/Tony a.k.a. 'Tonita')
Thursday, June 18, 2015
Pre-meeting for Journal Club presenters with Dr. B - 12:00 in his office.
Read journal article
Remove plates from incubator and move to fridge (for those that did transformation yesterday)
RE Digest
Analyze DNA Sequence Exercise as a group ?
Input information about which culture of plasmid you have (or will) grow up.
GoogleDocs/Misc/Plasmid Concentrations
https://docs.google.com/spreadsheet/ccc?key=0AoO2KqKh2q_-dENvNGJEdW9qdUxQZmFYeTVoeXA0SUE&usp=sharing
Friday, June 19, 2015
Lab Group Meeting @ 1 pm
GEA 1002nd Journal Club
Input information about which culture of plasmid you have (or will) grow up.
GoogleDocs/Misc/Plasmid Concentrations
https://docs.google.com/spreadsheet/ccc?key=0AoO2KqKh2q_-dENvNGJEdW9qdUxQZmFYeTVoeXA0SUE&usp=sharing
Biohazard Waste Boxing Demonstration - by John G.
Make and run gel for RE Digest (use Agarose Gel protocol)
????
My first PCR - Group 1
My first PCR - Group 2 (if time)
Target Discovery selections
Protocol Primer Design OverlapAssembly
Order Overlap Primers for class
On Your Targets Page:
Add Link to DNA Works output text fileAdd substrate cost, quantity, and catalog numbers (and supplier) for enzyme assay reagents
Add image of BRENDA reaction mechanism (screenshot it)
Update your lab notebook for this Week - ALL
Update your weekly Wikispaces Research page - ALL
Saturday, June 20, 2015
Sunday, June 21, 2015
Thursday, June 25, 2015
VisLab Tour @ 2 pm POB 2.404
Lab Group Meeting @ 1 pm
GEA 1001st Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups)
Zolli-Juran, M.; Cechetto, J. D.; Hartlen, R.; Daigle, D. M.; Brown, E. D., High throughput screening identifies novel inhibitors of Escherichia coli dihydrofolate reductase that are competitive with dihydrofolate. Bioorganic & Medicinal Chemistry Letters 2003, 13 (15), 2493-2496.
Zolli_JuranDHFRbacteriaHTSBioorgMedChemLett2003.pdf
Post data/results to your Wikispaces page - Summer15
update your Google Page in the Google Drive folder /VDSclass/ResearchPages - this will automatically update the Wiki
REQUIRED ITEMS FOR NOTEBOOKS:
All practice cloning work (including well labelled gels)
Protein Expression Schedule for this week (Mon June 22nd & Tues June 23rd)
https://docs.google.com/spreadsheets/d/1XedpP7OwNGjScpWtrpGTCX3dmFoTV0UA3v4-BL4jsaI/edit?usp=sharing
Week 3
Monday, June 22, 2015protein expressions in Groups
Tuesday, June 23, 2015
protein expressions in Groups, con't.....
Wednesday, June 24, 2015
- HOSA - Nikki, Charina
Middle Schoolers visit lab (2-4 pm)
Make Homemade SDS-Page gels (stagger) - how many plates do we have?
Target selection & Ordering Primers
Make buffers for purification - stagger
My First PCR - stagger (maybe)
Thursday, June 25, 2015
- HOSA - Nikki, Charina
Make Homemade SDS-Page gels (stagger) - how many plates do we have?
Make buffers for purification - stagger
Purifications
My First PCR - stagger
TACC VisLab Tour @ 2 pm POB 2.404
Friday, June 26, 2015
- HOSA - Nikki, Charina
Lab Group Meeting @ 1 pm
GEA 100Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups)
Journal Club Summ 15
Post data/results to your Wikispaces page - Summer15
update your Google Page in the Google Drive folder /VDSclass/ResearchPages - this will automatically update the Wiki
Purifications
Target Disco con't.....
Oligo Primer Design
Purifications
REQUIRED ITEMS FOR NOTEBOOKS:
All practice cloning work (including well labelled gels)
Protein work (esp protein gel and FPLC output and nanodrop)
We definitely need all of your Target work to be present in the notebook.
Saturday, June 27, 2015
Sunday, June 28, 2015
Week 4
Monday, June 29, 2015Lab Hours totaling (Charina or Nikki)
Wikispaces check - Nikki (put commments on each one)
Notebook check - Charina
FPLC - Matthew S. (and other VDSers will watch to learn the process - and get a 'See One' checkoff)
Transform, grow up in 160ml of LB+Kan, Midi-prep:
Diane - IMP-7 in pET28b
Anthony - KPC2 in pet24a
Simone - VIM2 in pet24a
Make SDS-PAGE gels - everyone that needs to
Run SDS-PAGE gels
Tuesday, June 30, 2015
My First PCR
Spin samples to prep for FPLC on Wed or Thurs
- store in 4degC
Wednesday, July 1, 2015
Target picking ?
TACC Tour
We will all meet at 1:00 pm to walk to the BUS together as a group.
We will be back on campus around 4 or 5pm
https://www.tacc.utexas.edu/about/contact
Thursday, July 2, 2015
FPLC
Lab Group Meeting @ 1 pm
GEA 100Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups)
Journal Club Summ 15
Update your notebook for the week
Post data/results to your Wikispaces page
- update your Google Page in the Google Drive folder /VDSclass/ResearchPages - this will automatically update the Wiki
Friday, July 3, 2015
Optional day - no new stuff, time to catch up on things you haven't gotten done.
Saturday, July 4, 2015 - Happy 4th of July!
Sunday, July 5, 2015
Week 5
OVERVIEW:
Monday, July 6, 2015
Lab Hours totaling (Nikki)
Target Selections - fill out form to select your target
Verify HIS tags on beta-metallo lactamases - Diane & Anthony & Simone
- use the Translation Map functinality of the Sequence Manipulation Suite to help
http://www.bioinformatics.org/sms2/index.html
- need a WORD document with highlighted regions
If your protein 'worked' from last week, then concentrate protein samples for FPLC.
The protein groups should work together. E.g. the two RpFabG groups would both concentrate their samples separately, but then combine them for FPLC.
FPLC - see FPLC ToDo groups above
Second Practice PCR (after you have done My First PCR successfully)
- PCR pLICsequencing15.xls
2:00 PM - Virtual Volunteers (NDM-1) in computer lab
- gather control compounds
- start some screening
What are the Magical Mystery Genes inside of pNIC-Bsa4?
- send pNIC-Bsa4 to sequencing using pLIC for and pLIC rev.
Start overnight cultures of 2nd Protein Expression
- (alternatively, start them in the morning depending on which Option you choose to do (A or B))
Tuesday, July 7, 2015
Start protein expression Round 2 - if you chose morning Option.
Continue PCRs
At end of day -
Wikispaces check.- due Tuesday night (Dr. B to check)
Notebook check
- Charina will check them after 6pm (put line with date and comments in each)
Wednesday, July 8, 2015
Stop Waste flow on FPLC Machine (Andee)
-check on pressure
Concentrate protein samples
FPLC - see FPLC ToDo groups abov
2-4 PM - Middle Schoolers visit lab - Lisa & Simone host
Thursday, July 9, 2015
12:00 - Fellowship photo shoot on front steps of PAI
Concentrate protein samples
FPLC - see FPLC ToDo groups above
4:00 pm - Tail Primer Design Session (in computer lab with Dr. B)
Friday, July 10, 2015
Lab Group Meeting @ 1 pm
GEA 100Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups)
Journal Club Summ 15
Update your notebook for the week
Post data/results to your Wikispaces page
- update your Google Page in the Google Drive folder /VDSclass/ResearchPages - this will automatically update the Wiki
2:15 - Lab Tour by Nikki for prospective students
3:30 PM - Virtual Volunteers (NDM-1) in computer lab
- gather control compounds
- set up proteins in GOLD
- start some screening
Oligo Primer dilution (each person makes their own Oligo Mix to use)
Saturday, July 11, 2015
Sunday, July 12, 2015
FPLC COMPLETED:
FPLC ToDo:
Week 6
OVERVIEW:
Week 6
Monday, July 13, 20151:00 - Virtual Volunteers NDM-1 virtual drug screening
- finish ligand prep for controls
- prep proteins in GOLD
- dock control ligands
- compare results for control set
- start runs of libraries
Paste your Tail primer sequences into the Targets spreadsheet
https://docs.google.com/spreadsheets/d/1dymtoVCnFwbX-kOaDWTyWh7KrQ5OZXLw5voZP9xaPb0/edit#gid=0
Oligo Primer dilution (each person makes their own Oligo Mix to use)
Primary PCR
Tuesday, July 14, 2015
Oligo Primer dilution (each person makes their own Oligo Mix to use)
Primary PCR
At end of day -
Wikispaces check.- due Tuesday night (Dr. B to check)
Notebook check
- Charina will check them after 6pm (put line with date and comments in each)
Wednesday, July 15, 2015
grow up ovenight culture of pNIC-Bsa4 (160ml of LB). Either save in freezer in the morning, or midi-prep it.
Thursday, July 16, 2015
3:20 - meet in lab and we'll walk over to PCL as a group
3:30- 4:30 PM - Roxanne Bogucka - Literature reading instruction activity (with the Aptamer stream! - PCL 1.124
Once you have your pNIC-Bsa4 sequencing back, What are the Magical Mystery Genes inside of pNIC-Bsa4?
- send pNIC-Bsa4 to sequencing using pLIC for and pLIC rev.
Friday, July 17, 2015
Lab Group Meeting @ 1 pm
GEA 100Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups)
Journal Club Summ 15
Work on Target Pages in Wkispaces (Target pages vs. Research Pages)
Saturday, July 18, 2015
Sunday, July 19, 2015
Week 7
OVERVIEW:- finish 2nd protein expression
- Make pNIC-Bsa4, midiprep it, send to sequencing, cut with BsaI for cloning
- sequence using pLIC for and pLIC rev.
- Make Pfu Polymerase
Monday, July 20, 20151:00 - Virtual Volunteers NDM-1 virtual drug screening
Tuesday, July 21, 2015
Yes, yes - the cloning protocol is finally uploaded to GDrive/Protocols
At end of day -
Wikispaces check.- due Tuesday night (Dr. B to check)
Notebook check
- Charina will check them after 6pm (put line with date and comments in each)
Wednesday, July 22, 2015
1 PM - Virtual Screening - generate a final list of NDM-1 inhibitor candidates
Thursday, July 23, 2015
UT Honors Colloquium for visiting HS students to UT - Lisa and Charina to attend and represent FRI.
1:00 - Virtual Volunteers - finalize NDM-1 list of compounds to submit to Dr. Fast
Documentary viewing at 4:00 in PAI 3.00? lecture hall
Friday, July 24, 2015
Lab Group Meeting @ 1 pm
GEA 100Journal Club (please read the journal club article prior to the next meeting so that we can discuss it in groups)
Journal Club Summ 15
Work on Target Pages in Wkispaces (Target pages vs. Research Pages)
Saturday, July 25, 2015
Sunday, July 26, 2015